A small collection of short scripts used to analyse intron stability in insects.
Based on innsect data taken from the Darwin Tree of Life Project.
Data Availability: DToL Respository
| File | Description |
|---|---|
| bladapter.py | Library to handle standard blast output. |
| get_sequences.py | Save full contig identified from a blast. |
| quick_seqs.py | Quickly save full contiq identified from a blast. |
| make_tree_fasta.py | Saves contig and sbjct sequence information ready for tree generation. |
| top_contigs.py | Saves the top hit for each species. |
| filter_contigs.py | Remove bad hits based on identities and expect value. |
An example pipeline may look as follows.
#add all species to a single fasta file
cat *.fasta > all_species.fasta
#initial engrailed search
makeblastdb -in all_species.fasta -dbtype nucl -out first_blastdb
tblastn -query engrailed.fasta -db first_blastdb -out prelim_blast.txt
#save top hit for each species
python3 top_contigs.py prelim_blast.txt prelim_top.txt
#search the full contig for top hits
python3 quick_seqs.py prelim_top.txt prelim_contigs.fasta